Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph lobSTR-workflow.cwl

https://github.com/common-workflow-language/cwlviewer.git

Path: src/test/resources/cwl/lobstr-v1/lobSTR-workflow.cwl

Branch/Commit ID: b58db216abe618f182edc4dbad7c53b7229ba625
workflow graph Bisulfite QC tools

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
workflow graph checkm_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_checkm_wnode.cwl

Branch/Commit ID: 1cfd46014be8d867044cb10d1ddde0cb3068ee84
workflow graph revsortlcase.cwl

https://github.com/ResearchObject/runcrate.git

Path: cwl/revsortlcase/revsortlcase.cwl

Branch/Commit ID: 19dee894600a1d265084f9187bfc1fe06b9f460b
workflow graph genome-kallisto-index.cwl

Generates a FASTA file with the DNA sequences for all transcripts in a GFF file and builds kallisto index

https://github.com/Barski-lab/workflows.git

Path: tools/genome-kallisto-index.cwl

Branch/Commit ID: 30e58892852641802b37912608fafbd8dc98918a
workflow graph Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

https://github.com/datirium/workflows.git

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f
workflow graph stdout-wf_v1_1.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/stdout-wf_v1_1.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
workflow graph count-lines18-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines18-wf.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph 1st-workflow.cwl

https://github.com/golharam/cwl-graph-generate.git

Path: test/1st-workflow.cwl

Branch/Commit ID: e39bdf429fa96a645d0995f153af22cac7a1bc38
workflow graph BWA index pipeline

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

https://github.com/datirium/workflows.git

Path: workflows/bwa-index.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16